ORCID Profile
0000-0002-0688-4260
Current Organisations
Helmholtz-Zentrum für Umweltforschung UFZ
,
University of Bristol
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Publisher: Helmholtz-Zentrum für Umweltforschung
Date: 2021
DOI: 10.48758/UFZ.11158
Publisher: MDPI AG
Date: 04-07-2017
DOI: 10.3390/NANO7070170
Publisher: Frontiers Media SA
Date: 07-07-2021
Abstract: During the past decades, several stand-alone and combinatorial methods have been developed to investigate the chemistry (i.e., mapping of elemental, isotopic, and molecular composition) and the role of microbes in soil and rhizosphere. However, none of these approaches are currently applicable to characterize soil-root-microbe interactions simultaneously in their spatial arrangement. Here we present a novel approach that allows for simultaneous microbial identification and chemical analysis of the rhizosphere at micro− to nano-meter spatial resolution. Our approach includes (i) a resin embedding and sectioning method suitable for simultaneous correlative characterization of Zea mays rhizosphere, (ii) an analytical work flow that allows up to six instruments/techniques to be used correlatively, and (iii) data and image correlation. Hydrophilic, immunohistochemistry compatible, low viscosity LR white resin was used to embed the rhizosphere s le. We employed waterjet cutting and avoided polishing the surface to prevent smearing of the s le surface at nanoscale. The quality of embedding was analyzed by Helium Ion Microscopy (HIM). Bacteria in the embedded soil were identified by Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH) to avoid interferences from high levels of autofluorescence emitted by soil particles and organic matter. Chemical mapping of the rhizosphere was done by Scanning Electron Microscopy (SEM) with Energy-dispersive X-ray analysis (SEM-EDX), Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS), nano-focused Secondary Ion mass Spectrometry (nanoSIMS), and confocal Raman spectroscopy (μ-Raman). High-resolution correlative characterization by six different techniques followed by image registration shows that this method can meet the demanding requirements of multiple characterization techniques to identify spatial organization of bacteria and chemically map the rhizosphere. Finally, we presented in idual and correlative workflows for imaging and image registration to analyze data. We hope this method will be a platform to combine various 2D analytics for an improved understanding of the rhizosphere processes and their ecological significance.
Publisher: Oxford University Press (OUP)
Date: 30-07-2021
Publisher: Elsevier BV
Date: 06-2016
DOI: 10.1016/J.MSEC.2016.02.053
Abstract: Preparation of hydroxyapatite coated custom-made metallic bone-implants is very important for the replacement of injured bones of the body. Furthermore, these bone-implants are more stable under the corrosive environment of the body and biocompatible than bone-implants made up of pure metals and metal alloys. Herein, we describe a novel, simple and low-cost technique to prepare biocompatible hydroxyapatite coated titanium metal (TiM) implants through growth of self-formed TiO2 thin-layer (SFTL) on TiM via a heat treatment process. SFTL acts as a surface binder of HA nanoparticles in order to produce HA coated implants. Colloidal HA nanorods prepared by a novel surfactant-assisted synthesis method, have been coated on SFTL via atomized spray pyrolysis (ASP) technique. The corrosion behavior of the bare and surface-modified TiM (SMTiM) in a simulated body fluid (SBF) medium is also studied. The highest corrosion rate is found to be for the bare TiM plate, but the corrosion rate has been reduced with the heat-treatment of TiM due to the formation of SFTL. The lowest corrosion rate is recorded for the implant prepared by heat treatment of TiM at 700 °C. The HA-coating further assists in the passivation of the TiM in the SBF medium. Both SMTiM and HA coated SMTiM are noncytotoxic against osteoblast-like (HOS) cells and are in high-bioactivity. The overall production process of bone-implant described in this paper is in high economic value.
Publisher: Frontiers Media SA
Date: 09-01-2023
Publisher: Queensland University of Technology
Date: 2017
Publisher: American Chemical Society (ACS)
Date: 16-02-2017
Abstract: Nanotextured surfaces (NTSs) are critical to organisms as self-adaptation and survival tools. These NTSs have been actively mimicked in the process of developing bactericidal surfaces for erse biomedical and hygiene applications. To design and fabricate bactericidal topographies effectively for various applications, understanding the bactericidal mechanism of NTS in nature is essential. The current mechanistic explanations on natural bactericidal activity of nanopillars have not utilized recent advances in microscopy to study the natural interaction. This research reveals the natural bactericidal interaction between E. coli and a dragonfly wing's (Orthetrum villosovittatum) NTS using advanced microscopy techniques and proposes a model. Contrary to the existing mechanistic models, this experimental approach demonstrated that the NTS of Orthetrum villosovittatum dragonfly wings has two prominent nanopillar populations and the resolved interface shows membrane damage occurred without direct contact of the bacterial cell membrane with the nanopillars. We propose that the bacterial membrane damage is initiated by a combination of strong adhesion between nanopillars and bacterium EPS layer as well as shear force when immobilized bacterium attempts to move on the NTS. These findings could help guide the design of novel biomimetic nanomaterials by maximizing the synergies between biochemical and mechanical bactericidal effects.
Publisher: Cold Spring Harbor Laboratory
Date: 05-02-2021
DOI: 10.1101/2021.02.05.429689
Abstract: During the past decades, several stand-alone and combinatory methods have been developed to investigate the chemistry (i.e. mapping of elemental, isotopic and molecular composition) and the role of microbes in soil and rhizosphere. However, none of these approaches are currently capable of characterizing soil-root-microbe interactions simultaneously in their spatial arrangement. Here we present a novel approach that allows chemical and microbial identification of the rhizosphere at micro-to nano-meter spatial resolution. Our approach includes i) a resin embedding and sectioning method suitable for simultaneous correlative characterization of Zea mays rhizosphere, ii) an analytical work flow that allows up to six instruments/techniques to be used correlatively, and iii) data and image correlation. Hydrophilic, immunohistochemistry compatible, low viscosity LR white resin was used to embed the rhizosphere s le. We employed waterjet cutting and avoided polishing the surface to prevent smearing of the s le surface at nanoscale. Embedding quality was analyzed by Helium Ion Microscopy (HIM). Bacteria in the embedded soil was identified by Catalyzed Reporter Deposition-Fluorescence In Situ Hybridization (CARD-FISH) to avoid interferences from high levels of auto fluorescence emitted by soil particles and organic matter. Chemical mapping of the rhizosphere was done by Scanning Electron Microscopy (SEM) with Energy-dispersive X-ray analysis (SEM-EDX), Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS), nano-focused Secondary Ion mass Spectrometry (nanoSIMS), and confocal Raman spectroscopy (µ-Raman). High-resolution correlative characterization by six different techniques followed by image registration shows that this method can meet the demanding requirements of multiple characterization techniques to chemically map the rhizosphere and identify spatial organization of bacteria. Finally, we presented in idual and correlative workflows for imaging and image registration to analyze data. We hope this method will be a platform to combine various 2D analytics for an le understanding of the rhizosphere processes and their ecological significance.
Publisher: Copernicus GmbH
Date: 27-03-2022
DOI: 10.5194/EGUSPHERE-EGU22-6207
Abstract: & & Correct image segmentation is the pre-requisite for identifying classes of objects in microscopic datasets in order to determine relationships between them. We recently reported on a novel embedding protocol for rhizosphere s les based on the hydrophilic acrylic LR-white resin.& sup& & /sup& X-ray & #181 -CT data measured on such embedded s les shows only minimal contrast between root and resin which renders segmentation of these data is difficult or even impossible using common methods based on thresholding of histograms or detection of edges.& & & & Here, we demonstrate how this barrier can be overcome using deep learning of convolutional neural networks based on U-Net architecture.& sup& & /sup& We show successfully segmented roots from resin, where classical machine learning approach Random Forest was not successful in our attempts. Firstly, the embedded s les were characterised by X-ray & #181 -CT and cut by a water-jet. Roots on the exposed 2D section were identified using epifluorescence and helium ion microscopy. The analysed 2D image plane was then correlated with the X-ray & #181 -CT data for accurate classification of training 3D image pixels. With a given input image (in this case a greyscale micrograph of resin embedded soil), a trained U-Net model with minimal labelled pixels, semantically segmented the X-ray data set showing roots, soil and pores. Using multiple deep learning algorithms, the U-Net was the most promising architecture to segment rhizosphere X-ray & #181 -CT and we show the different input parameters which can improve the segmentation process. The deep learning experiment was carried out with the ORS dragonfly image processing software. We show an accurate and fast approach that can be used to segment LR-white embedded rhizosphere X-ray CT data to roots-soil-and pores for further correlative microscopy analysis to interpret complex rhizosphere processes in the future.& & & & & strong& Author Contributions:& /strong& & CB embedded the soil s les and trained the deep learning algorithms, Eva Lippold acquired and reconstructed CT data, Matthias Schmidt acquired helium ion microscopy data and discussions on improving data segmentation.& & & & & strong& Acknowledgement:& /strong& This work was conducted within the framework of the priority program 2089, & #8220 Rhizosphere spatiotemporal organization-a key to rhizosphere functions& #8221 funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) & #8211 Project number RI-903/7-1. Funding is acquired by Niculina Musat and Hans Richnow. Authors acknowledge the analytical facilities of the Centre for Chemical Microscopy (ProVIS) at the Helmholtz Centre for Environmental Research, Leipzig, Germany, which is supported by the European Regional Development Funds (EFRE - Europe funds Saxony) and the Helmholtz Association. Authors thank Object Research Systems for providing a free Dragonfly commercial licence for use in this work.& & & & & strong& References& /strong& & & & ul& & li& Bandara, C. D. Schmidt, M. & Davoudpour, Y. & Stryhanyuk, H. & Richnow, H. H. Musat, N., Microbial Identification, High-Resolution Microscopy and Spectrometry of the Rhizosphere in Its Native Spatial Context. & em& Frontiers in Plant Science & /em& & strong& ,& /strong& & em& & /em& (1195).& /li& & li& Ronneberger, O., Fischer, P., Brox, T. U-Net: Convolutional Networks for Biomedical Image Segmentation 2015.& /li& & /ul&
Publisher: Copernicus GmbH
Date: 04-03-2021
DOI: 10.5194/EGUSPHERE-EGU21-12160
Abstract: & & Studying the spatial distribution of bacteria and characterizing the soil chemistry (i.e., elemental, isotopic and molecular composition) underpins the comprehensive understanding of rhizosphere associated processes. During the past decades, several stand-alone methods have been developed to investigate soil chemistry, nutrient cycling and plant nutrition. However, in idual approaches as stand-alone are not capable of providing an overall rhizosphere processes involving soil, root and microbes in a spatial context, as there is no common s le preparation method available to satisfy in idual needs of each technique. Here, we present i) a s le preparation method, which includes soil embedding, sectioning and ii)& a correlative imaging and image registration workflow, which allows for characterization of minerals, roots and microbes by different high-resolution imaging and microanalytical techniques. This allows for conducting rhizosphere studies on different scales, focusing on root-soil-microbe interfaces with spatial resolution of nano-meter scale. Hydrophilic, immunohistochemistry compatible, low viscosity LR White resin was used to embed and stabilize the soil and make it ultra-high vacuum compatible. We employed water-jet cutting as a novel approach to slice the embedded s les, and, by doing so, avoided polishing of the surface which often leads to translocation of s le material (smearing). The quality of this embedding was analyzed by and Helium Ion Microscopy (HIM). Epifluorescence microscopy in combination with Catalyzed Reporter Deposition-Fluorescence in-situ Hybridization (CARD-FISH) was employed to accurately identify and determine the spatial distribution of bacteria in the embedded s le, thus avoiding ambiguities from high levels of auto-fluorescence emitted by soil particles and organic matter. Chemical mapping of the rhizosphere was acquired by SEM/EDX, ToF-SIMS, nanoSIMS for elemental, molecular and isotopic characterization, respectively, and & #181 -Raman microscopy for specific identification of minerals.& & & & In summary, we demonstrate that LR White embedding and water-jet cutting of soil in combination with CARD-FISH and a correlative microscopic workflow, allows for a comprehensive characterization of biotic and abiotic components in the rhizosphere. The developed s le preparation method can facilitate the various requirements of involved microscopy techniques and in idual workflows for imaging and image registration to analyze data. We foresee that this approach will establish an excellent platform to study various soil processes and synergistic understanding of complex rhizosphere processes.& &
Publisher: American Chemical Society (ACS)
Date: 09-06-2020
Publisher: Wiley
Date: 30-07-2013
DOI: 10.1002/APP.39601
Publisher: Elsevier BV
Date: 09-2013
Publisher: SAGE Publications
Date: 28-10-2014
Abstract: In this study, the response of different filler loadings (5–20 wt%) of zinc oxide nanoparticles reinforced ultra-high molecular weight polyethylene on the mechanical, tribological and antibacterial performances were attempted. The compression, tensile and micro-hardness properties of the nano-zinc oxide/ultra-high molecular weight polyethylene composites were studied. The tribological properties were investigated using DUCOM pin-on-disc tester with variable applied loads (5–35 N) and sliding speeds (0.209 m/s and 0.419 m/s) against 1200 grit size silicon carbide abrasive paper under dry sliding conditions. The worn surfaces and transfer films of the composites were observed using the scanning electron microscopy. Experimental results show that reinforcing ultra-high molecular weight polyethylene with zinc oxide nanoparticles would improve certain mechanical and tribological properties. Wear performance was enhanced with maximum wear resistance found at 10 wt% nano-zinc oxide/ultra-high molecular weight polyethylene composite. The average coefficient of friction of ultra-high molecular weight polyethylene shows a decrease after reinforcement with zinc oxide nanoparticles. Upon zinc oxide nanoparticles reinforcement, the worn surface shows reduced severity of wear. The nano-zinc oxide/ultra-high molecular weight polyethylene composite imparts antibacterial activity against Escherichia coli and Staphylococcus aureus.
Publisher: Informa UK Limited
Date: 15-07-2013
Location: Sri Lanka
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Chiththaka Bandara.